RMplex reveals population differences in RM Y-STR mutation rates and provides improved father-son differentiation in Japanese

Otagiri, Tomomi; Sato, Noriko; Asamura, Hideki; Parvanova, Evelina; Kayser, Manfred; Ralf, Arwin

doi:10.1016/j.fsigen.2022.102766

Cited by 5 publications

(4 citation statements)

References 23 publications

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“…In the current pedigree study, we empirically showed that the 99% differentiation rate was reached with RMplex (including those 26 RM Y-STRs) from nine meioses onwards, closely agreeing with the previous theoretical expectation. Notably, our study is the first that demonstrates male relative differentiation in appreciable numbers for distant relatives separated by more than two meioses for the full set of 30 RMplex Y-STRs, previously only father-son pairs and a limited number of brothers were described (Neuhuber et al 2022;Otagiri et al 2022). Male relative differentiation of males separated by three to four meioses were only available for a subset of 13 RM Y-STRs (Adnan et al 2016), and reliable data (i.e., with sufficient sample size) about Y-STR differentiation of males separated by more than four meioses was lacking completely.…”

Section: Male Relative Differentiation Ratesmentioning

confidence: 75%

“…The different mutation rate estimates could also be caused by stochastic effects, or could be a result of the different biogeographic origin of the subject of the different studies. As longer alleles (i.e., longest uninterrupted stretch, LUS) tend to mutate more frequently than their shorter counterparts and because different populations (i.e., different haplogroups) can exhibit different allelic distributions, some populations may exhibit remarkably high of low mutability for specific Y-STRs (Claerhout et al 2018 ; Otagiri et al 2022 ). The overall high concordance between father–son based and pedigree based mutation rates suggest that using pedigrees is a valid approach to estimate mutation rates.…”

Section: Discussionmentioning

confidence: 99%

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Large-scale pedigree analysis highlights rapidly mutating Y-chromosomal short tandem repeats for differentiating patrilineal relatives and predicting their degrees of consanguinity

et al. 2022

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Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were suggested for differentiating patrilineally related men as relevant in forensic genetics, anthropological genetics, and genetic genealogy. Empirical data are available for closely related males, while differentiation rates for more distant relatives are scarce. Available RM Y-STR mutation rate estimates are typically based on father–son pair data, while pedigree-based studies for efficient analysis requiring less samples are rare. Here, we present a large-scale pedigree analysis in 9379 pairs of men separated by 1–34 meioses on 30 Y-STRs with increased mutation rates including all known RM Y-STRs (RMplex). For comparison, part of the samples were genotyped at 25 standard Y-STRs mostly with moderate mutation rates (Yfiler Plus). For 43 of the 49 Y-STRs analyzed, pedigree-based mutation rates were similar to previous father–son based estimates, while for six markers significant differences were observed. Male relative differentiation rates from the 30 RMplex Y-STRs were 43%, 84%, 96%, 99%, and 100% for relatives separated by one, four, six, nine, and twelve meioses, respectively, which largely exceeded rates obtained by 25 standard Y-STRs. Machine learning based models for predicting the degree of patrilineal consanguinity yielded accurate and reasonably precise predictions when using RM Y-STRs. Fully matching haplotypes resulted in a 95% confidence interval of 1–6 meioses with RMplex compared to 1–25 with Yfiler Plus. Our comprehensive pedigree study demonstrates the value of RM Y-STRs for differentiating male relatives of various types, in many cases achieving individual identification, thereby overcoming the largest limitation of forensic Y-chromosome analysis.

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Section: Male Relative Differentiation Ratesmentioning

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Large-scale pedigree analysis highlights rapidly mutating Y-chromosomal short tandem repeats for differentiating patrilineal relatives and predicting their degrees of consanguinity

et al. 2022

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“…The median number of pairwise differences (Rst) could then be used as a measure of diversity. This method allows for comparisons of differences between Y-STR marker sets or different populations, even in the absence of shared haplotypes, as demonstrated in a previous study [11].…”

Section: Recognizing Pairwise Mutationsmentioning

confidence: 93%

“…Using Y-STRs of different mutation rates in principle allows for the investigation of events that occurred at different time scales. A recent study suggested that Y-STR mutation rates are influenced by the haplogroup and population background [11], which require further research through more Y-STR mutation rate studies in different populations that include Y-SNP haplogroup analyses.…”

Section: Introductionmentioning

confidence: 99%

Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses

Ralf,

van Wersch,

Montiel González

et al. 2024

Genes

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Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic, genealogical, and population genetics. With the recent increase in the number of rapidly mutating (RM) Y-STRs, an unprecedented level of male differentiation can be achieved, widening and improving the applications of Y-STRs in various fields, including forensics. The growing complexity of Y-STR data increases the need for automated data analyses, but dedicated software tools are scarce. To address this, we present the Male Pedigree Toolbox (MPT), a software tool for the automated analysis of Y-STR data in the context of patrilineal genealogical relationships. The MPT can estimate mutation rates and male relative differentiation rates from input Y-STR pedigree data. It can aid in determining ancestral haplotypes within a pedigree and visualize the genetic variation within pedigrees in all branches of family trees. Additionally, it can provide probabilistic classifications using machine learning, helping to establish or prove the structure of the pedigree and the level of relatedness between males, even for closely related individuals with highly similar haplotypes. The tool is flexible and easy to use and can be adjusted to any set of Y-STR markers by modifying the intuitive input file formats. We introduce the MPT software tool v1.0 and make it publicly available with the goal of encouraging and supporting forensic, genealogical, and other geneticists in utilizing the full potential of Y-STRs for both research purposes and practical applications, including criminal casework.

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Analysis of rapidly mutating Y-STRs enables almost complete discrimination of unrelated and related males from the African continent

Barni,

Ralf,

Della Rocca

et al. 2024

Forensic Science International: Genetics

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RMplex reveals population differences in RM Y-STR mutation rates and provides improved father-son differentiation in Japanese

Cited by 5 publications

References 23 publications

Large-scale pedigree analysis highlights rapidly mutating Y-chromosomal short tandem repeats for differentiating patrilineal relatives and predicting their degrees of consanguinity

Large-scale pedigree analysis highlights rapidly mutating Y-chromosomal short tandem repeats for differentiating patrilineal relatives and predicting their degrees of consanguinity

Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses

Analysis of rapidly mutating Y-STRs enables almost complete discrimination of unrelated and related males from the African continent

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